The rheological properties of ferrofluids are related to various applications, such as sealing and loudspeakers, and have therefore attracted widespread attention. However, the rheological properties and their influence on the mechanisms of perfluoropolyether oil (PFPE oil)-based ferrofluids are complicated and not clear. Here, a series of PFPE oil-based ferrofluids were synthesized via a chemical co-precipitation method, and their rheological properties were revealed, systematically. The results indicate that the prepared Zn-ferrite particles have an average size of 12.1 nm, within a range of 4–18 nm, and that the ferrofluids have excellent dispersion stability. The activity of the ferrofluids changes from Newtonian to non-Newtonian, then to solid-like with increasing w from 10 wt% to 45.5 wt%, owing to their variation in microstructures. The viscosity of the ferrofluids increases with increasing Mw (the molecular weight of base liquid PFPE oil polymer), attributed to the increase in entanglements between PFPE oil molecules. The magnetization temperature variation of Zn-ferrite nanoparticles and viscosity temperature variation of PFPE oil together contribute to the viscosity temperature change in ferrofluids. The viscosity of the ferrofluids basically remains unchanged when shear rate is above 50 s−1, with increasing magnetic field strength; however, it first increases and then levels off when the rate is under 10 s−1, revealing that the shear rate and magnetic field strength together affect viscosity. The viscosity and its alteration in Zn-ferrite/PFPE oil-based ferrofluids could be deduced through our work, which will be greatly significant in basic theoretical research and in various applications.